[Gmod-ajax] Adding track metadata tags at processing time?

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[Gmod-ajax] Adding track metadata tags at processing time?

Chris Childers
Hi all,

We've been hand editing our track configuration files to add metadata, and I would prefer to be able to define track level metadata at the time of loading, so that my trackList.json looks more like the example below.  Is there a way to invoke flatfile_to_json.pl that will let us add our metadata like this?  There are other browsers that have tracks modeled this way, and I was just curious if they were handled post processing, or if there is a flag I've been missing in the JBrowse configuration guide.

Thanks,
Chris

      {
         "style" : {
              "style_options":  "style goes here"
            },
         },
         "metadata" : {
"Track information": "Gene models",
"Data provider":"Data Guru",
"Source of materials": "Libraries (stages 3, 5, 7, and 10)",
"Analysis method": "Mapped the RNA-seq reads with BLAT"
        },
         "key" : "gene.model",
         "label" : "Gene Models"
      }

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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Re: Adding track metadata tags at processing time?

Colin
The --config parameter of flatfile-to-json can take this metadata. Is this what your were interested in?

bin/flatfile-to-json.pl --gff yourgff.gff3 --config '{ "metadata": { "Track information": "Gene models", "Data provider":"Data Guru", "Source of materials": "Libraries (stages 3, 5, 7, and 10)", "Analysis method": "Mapped the RNA-seq reads with BLAT" } }' --trackLabel OGS

-Colin




On Thu, Jul 3, 2014 at 10:30 AM, Chris Childers <[hidden email]> wrote:
Hi all,

We've been hand editing our track configuration files to add metadata, and I would prefer to be able to define track level metadata at the time of loading, so that my trackList.json looks more like the example below.  Is there a way to invoke flatfile_to_json.pl that will let us add our metadata like this?  There are other browsers that have tracks modeled this way, and I was just curious if they were handled post processing, or if there is a flag I've been missing in the JBrowse configuration guide.

Thanks,
Chris

      {
         "style" : {
              "style_options":  "style goes here"
            },
         },
         "metadata" : {
"Track information": "Gene models",
"Data provider":"Data Guru",
"Source of materials": "Libraries (stages 3, 5, 7, and 10)",
"Analysis method": "Mapped the RNA-seq reads with BLAT"
        },
         "key" : "gene.model",
         "label" : "Gene Models"
      }

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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Re: Adding track metadata tags at processing time?

Chris Childers
Hi Colin,

That's exactly what I was looking for.  I did not see that in any of the documentation I could find.  Is there another resource I missed?

Thanks!
Chris


On Mon, Jul 7, 2014 at 11:36 AM, Colin <[hidden email]> wrote:
The --config parameter of flatfile-to-json can take this metadata. Is this what your were interested in?

bin/flatfile-to-json.pl --gff yourgff.gff3 --config '{ "metadata": { "Track information": "Gene models", "Data provider":"Data Guru", "Source of materials": "Libraries (stages 3, 5, 7, and 10)", "Analysis method": "Mapped the RNA-seq reads with BLAT" } }' --trackLabel OGS

-Colin




On Thu, Jul 3, 2014 at 10:30 AM, Chris Childers <[hidden email]> wrote:
Hi all,

We've been hand editing our track configuration files to add metadata, and I would prefer to be able to define track level metadata at the time of loading, so that my trackList.json looks more like the example below.  Is there a way to invoke flatfile_to_json.pl that will let us add our metadata like this?  There are other browsers that have tracks modeled this way, and I was just curious if they were handled post processing, or if there is a flag I've been missing in the JBrowse configuration guide.

Thanks,
Chris

      {
         "style" : {
              "style_options":  "style goes here"
            },
         },
         "metadata" : {
"Track information": "Gene models",
"Data provider":"Data Guru",
"Source of materials": "Libraries (stages 3, 5, 7, and 10)",
"Analysis method": "Mapped the RNA-seq reads with BLAT"
        },
         "key" : "gene.model",
         "label" : "Gene Models"
      }

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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Re: Adding track metadata tags at processing time?

Colin
That parameter is described in the flatfile-to-json.pl --help. Unfortunately, the best documentation on the web for jbrowse is the configuration guide which doesn't necessarily include the details about the command line scripts and setup.

-Colin



On Mon, Jul 7, 2014 at 10:40 AM, Chris Childers <[hidden email]> wrote:
Hi Colin,

That's exactly what I was looking for.  I did not see that in any of the documentation I could find.  Is there another resource I missed?

Thanks!
Chris


On Mon, Jul 7, 2014 at 11:36 AM, Colin <[hidden email]> wrote:
The --config parameter of flatfile-to-json can take this metadata. Is this what your were interested in?

bin/flatfile-to-json.pl --gff yourgff.gff3 --config '{ "metadata": { "Track information": "Gene models", "Data provider":"Data Guru", "Source of materials": "Libraries (stages 3, 5, 7, and 10)", "Analysis method": "Mapped the RNA-seq reads with BLAT" } }' --trackLabel OGS

-Colin




On Thu, Jul 3, 2014 at 10:30 AM, Chris Childers <[hidden email]> wrote:
Hi all,

We've been hand editing our track configuration files to add metadata, and I would prefer to be able to define track level metadata at the time of loading, so that my trackList.json looks more like the example below.  Is there a way to invoke flatfile_to_json.pl that will let us add our metadata like this?  There are other browsers that have tracks modeled this way, and I was just curious if they were handled post processing, or if there is a flag I've been missing in the JBrowse configuration guide.

Thanks,
Chris

      {
         "style" : {
              "style_options":  "style goes here"
            },
         },
         "metadata" : {
"Track information": "Gene models",
"Data provider":"Data Guru",
"Source of materials": "Libraries (stages 3, 5, 7, and 10)",
"Analysis method": "Mapped the RNA-seq reads with BLAT"
        },
         "key" : "gene.model",
         "label" : "Gene Models"
      }

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax





------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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Re: Adding track metadata tags at processing time?

Chris Childers
I see that now.

Thanks!


On Mon, Jul 7, 2014 at 11:57 AM, Colin <[hidden email]> wrote:
That parameter is described in the flatfile-to-json.pl --help. Unfortunately, the best documentation on the web for jbrowse is the configuration guide which doesn't necessarily include the details about the command line scripts and setup.

-Colin



On Mon, Jul 7, 2014 at 10:40 AM, Chris Childers <[hidden email]> wrote:
Hi Colin,

That's exactly what I was looking for.  I did not see that in any of the documentation I could find.  Is there another resource I missed?

Thanks!
Chris


On Mon, Jul 7, 2014 at 11:36 AM, Colin <[hidden email]> wrote:
The --config parameter of flatfile-to-json can take this metadata. Is this what your were interested in?

bin/flatfile-to-json.pl --gff yourgff.gff3 --config '{ "metadata": { "Track information": "Gene models", "Data provider":"Data Guru", "Source of materials": "Libraries (stages 3, 5, 7, and 10)", "Analysis method": "Mapped the RNA-seq reads with BLAT" } }' --trackLabel OGS

-Colin




On Thu, Jul 3, 2014 at 10:30 AM, Chris Childers <[hidden email]> wrote:
Hi all,

We've been hand editing our track configuration files to add metadata, and I would prefer to be able to define track level metadata at the time of loading, so that my trackList.json looks more like the example below.  Is there a way to invoke flatfile_to_json.pl that will let us add our metadata like this?  There are other browsers that have tracks modeled this way, and I was just curious if they were handled post processing, or if there is a flag I've been missing in the JBrowse configuration guide.

Thanks,
Chris

      {
         "style" : {
              "style_options":  "style goes here"
            },
         },
         "metadata" : {
"Track information": "Gene models",
"Data provider":"Data Guru",
"Source of materials": "Libraries (stages 3, 5, 7, and 10)",
"Analysis method": "Mapped the RNA-seq reads with BLAT"
        },
         "key" : "gene.model",
         "label" : "Gene Models"
      }

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax






------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax